diff --git a/tests/hash-backend-integration/package.json b/tests/hash-backend-integration/package.json
index 8df50911c8a..3eb829df0b1 100644
--- a/tests/hash-backend-integration/package.json
+++ b/tests/hash-backend-integration/package.json
@@ -10,7 +10,7 @@
     "fix:eslint": "eslint --fix .",
     "lint:eslint": "eslint --report-unused-disable-directives .",
     "lint:tsc": "tsc --noEmit",
-    "test:integration": "vitest --run"
+    "test:integration": "vitest --run && vitest --run --config vitest.snapshot.config.ts"
   },
   "dependencies": {
     "@apps/hash-api": "workspace:*",
diff --git a/tests/hash-backend-integration/src/tests/admin-server.ts b/tests/hash-backend-integration/src/tests/admin-server.ts
index 5ae6dbbefe1..d884473f3e4 100644
--- a/tests/hash-backend-integration/src/tests/admin-server.ts
+++ b/tests/hash-backend-integration/src/tests/admin-server.ts
@@ -6,6 +6,25 @@ import { StatusCode } from "@local/status";
 
 import type { GraphStatus } from "@rust/hash-graph-type-defs/typescript/status";
 
+/**
+ * Throw unless running in the snapshot group of the backend integration
+ * tests.
+ *
+ * Destructive graph operations wipe the shared system graph that the seeded
+ * group (`vitest.config.ts`) seeds once per run via `globalSetup`, so they
+ * may only run in the snapshot group (`vitest.snapshot.config.ts`), which
+ * runs as a separate vitest invocation after the seeded group and owns the
+ * wipe. The snapshot group's config sets the `HASH_TEST_GROUP` marker checked
+ * here.
+ */
+const assertRunningInSnapshotGroup = (operation: string) => {
+  if (process.env.HASH_TEST_GROUP !== "snapshot") {
+    throw new Error(
+      `\`${operation}\` wipes the graph and may only run in the snapshot group of the backend integration tests, which runs as a separate vitest invocation after the seeded group so it cannot destroy the system graph seeded by \`globalSetup\`. To make a test file destructive, place it under \`src/tests/subgraph/\` so that \`vitest.snapshot.config.ts\` picks it up.`,
+    );
+  }
+};
+
 // eslint-disable-next-line @typescript-eslint/prefer-nullish-coalescing
 const port = process.env.HASH_GRAPH_ADMIN_PORT || "4001";
 
@@ -96,8 +115,13 @@ export const deleteEntities = async () => {
 
 /**
  * Restore a snapshot from a file.
+ *
+ * May only be called from the snapshot group of the backend integration
+ * tests (`vitest.snapshot.config.ts`).
  */
 export const restoreSnapshot = async (snapshotPath: string) => {
+  assertRunningInSnapshotGroup("restoreSnapshot");
+
   await fetch(`http://127.0.0.1:${port}/snapshot`, {
     method: "POST",
     body: createReadStream(snapshotPath),
@@ -137,8 +161,13 @@ export const deleteUser = async (
  * Reset the Graph.
  *
  * This is a convenience function for deleting all entities, entity types, property types, data types, and accounts.
+ *
+ * May only be called from the snapshot group of the backend integration
+ * tests (`vitest.snapshot.config.ts`).
  */
 export const resetGraph = async () => {
+  assertRunningInSnapshotGroup("resetGraph");
+
   await deleteEntities();
   await deleteEntityTypes();
   await deletePropertyTypes();
diff --git a/tests/hash-backend-integration/tsconfig.json b/tests/hash-backend-integration/tsconfig.json
index 8ff51e490d6..31ae08d6037 100644
--- a/tests/hash-backend-integration/tsconfig.json
+++ b/tests/hash-backend-integration/tsconfig.json
@@ -1,4 +1,9 @@
 {
   "extends": "@local/tsconfig/legacy-base-tsconfig-to-refactor.json",
-  "include": ["./src/", "codegen.config.ts", "vitest.config.ts"]
+  "include": [
+    "./src/",
+    "codegen.config.ts",
+    "vitest.config.ts",
+    "vitest.snapshot.config.ts"
+  ]
 }
diff --git a/tests/hash-backend-integration/vitest.config.ts b/tests/hash-backend-integration/vitest.config.ts
index 83ada709987..9339a6e9bcd 100644
--- a/tests/hash-backend-integration/vitest.config.ts
+++ b/tests/hash-backend-integration/vitest.config.ts
@@ -1,29 +1,48 @@
 /// <reference types="vitest" />
 import { defineConfig } from "vitest/config";
-import { BaseSequencer } from "vitest/node";
 
-import type { TestSpecification } from "vitest/node";
+import type { TestUserConfig } from "vitest/config";
 
 /**
- * The subgraph tests reset the graph and restore standalone snapshots,
- * destroying the shared system graph seeded once per run by `globalSetup`.
- * Sort them after all other test files so that they cannot break tests which
- * rely on the shared seed – the next run's `globalSetup` re-seeds the graph
- * from scratch.
+ * The backend integration tests are split into two groups which run as
+ * separate, sequential vitest invocations (see the `test:integration` script
+ * in `package.json`):
+ *
+ * - the seeded group (this config, `src/tests/graph/`): runs against the
+ *   shared system graph seeded once per run by `globalSetup` and must never
+ *   wipe it, and
+ * - the snapshot group (`vitest.snapshot.config.ts`, `src/tests/subgraph/`):
+ *   wipes the graph and restores standalone snapshots, so it runs after the
+ *   seeded group.
+ *
+ * These test options are shared between the two configs.
  */
-class DestructiveTestsLastSequencer extends BaseSequencer {
-  override async sort(files: TestSpecification[]) {
-    const isDestructive = (file: TestSpecification) =>
-      file.moduleId.includes("/src/tests/subgraph/");
-
-    const sorted = await super.sort(files);
-
-    return [
-      ...sorted.filter((file) => !isDestructive(file)),
-      ...sorted.filter(isDestructive),
-    ];
-  }
-}
+export const sharedTestConfig = {
+  coverage: {
+    enabled: process.env.TEST_COVERAGE === "true",
+    provider: "istanbul",
+    reporter: ["lcov", "text"],
+    include: ["**/*.{c,m,}{j,t}s{x,}"],
+    exclude: ["**/node_modules/**", "**/dist/**"],
+  },
+  setupFiles: [
+    "@local/hash-backend-utils/environment",
+    "./src/tests/setup-opentelemetry.ts",
+  ],
+  environment: "node",
+  testTimeout: 60_000,
+  hookTimeout: 120_000,
+  sequence: {
+    hooks: "list",
+  },
+  /**
+   * These integration tests share a single graph instance, so running files
+   * in parallel causes graph state races.
+   */
+  fileParallelism: false,
+  maxWorkers: 1,
+  maxConcurrency: 1,
+} satisfies TestUserConfig;
 
 export default defineConfig({
   plugins: [],
@@ -31,35 +50,8 @@ export default defineConfig({
     target: "esnext",
   },
   test: {
-    coverage: {
-      enabled: process.env.TEST_COVERAGE === "true",
-      provider: "istanbul",
-      reporter: ["lcov", "text"],
-      include: ["**/*.{c,m,}{j,t}s{x,}"],
-      exclude: ["**/node_modules/**", "**/dist/**"],
-    },
+    ...sharedTestConfig,
     globalSetup: ["./src/tests/global-setup.ts"],
-    setupFiles: [
-      "@local/hash-backend-utils/environment",
-      "./src/tests/setup-opentelemetry.ts",
-    ],
-    include: [
-      "src/tests/graph/**/*.test.ts",
-      "src/tests/subgraph/**/*.test.ts",
-    ],
-    environment: "node",
-    testTimeout: 60_000,
-    hookTimeout: 120_000,
-    sequence: {
-      hooks: "list",
-      sequencer: DestructiveTestsLastSequencer,
-    },
-    /**
-     * These integration tests share a single graph instance, so running files
-     * in parallel causes graph state races.
-     */
-    fileParallelism: false,
-    maxWorkers: 1,
-    maxConcurrency: 1,
+    include: ["src/tests/graph/**/*.test.ts"],
   },
 });
diff --git a/tests/hash-backend-integration/vitest.snapshot.config.ts b/tests/hash-backend-integration/vitest.snapshot.config.ts
new file mode 100644
index 00000000000..c3f6530a690
--- /dev/null
+++ b/tests/hash-backend-integration/vitest.snapshot.config.ts
@@ -0,0 +1,44 @@
+/// <reference types="vitest" />
+import { defineConfig } from "vitest/config";
+
+import { sharedTestConfig } from "./vitest.config";
+
+/**
+ * Config for the snapshot group of the backend integration tests: the test
+ * files under `src/tests/subgraph/` wipe the graph via `resetGraph` and
+ * restore standalone snapshots via `restoreSnapshot`, so they cannot share
+ * the system graph seeded by the seeded group's `globalSetup`.
+ *
+ * The `test:integration` script in `package.json` runs this config as a
+ * separate vitest invocation after the seeded group (`vitest.config.ts`), so
+ * the seeded group structurally cannot lose its seed to these tests. There is
+ * deliberately no `globalSetup` here – each test file restores the snapshot
+ * it needs, and the next seeded run re-seeds the graph from scratch.
+ *
+ * To make a test file destructive, place it under `src/tests/subgraph/` so
+ * this config picks it up. Destructive graph operations refuse to run outside
+ * this group: `resetGraph`/`restoreSnapshot` in `src/tests/admin-server.ts`
+ * throw unless the `HASH_TEST_GROUP` marker below is set.
+ */
+export default defineConfig({
+  plugins: [],
+  build: {
+    target: "esnext",
+  },
+  test: {
+    ...sharedTestConfig,
+    coverage: {
+      ...sharedTestConfig.coverage,
+      /**
+       * Written next to the seeded group's `./coverage` – vitest cleans its
+       * reports directory at the start of a run, so sharing one directory
+       * would discard the seeded group's report.
+       */
+      reportsDirectory: "./coverage-snapshot",
+    },
+    include: ["src/tests/subgraph/**/*.test.ts"],
+    env: {
+      HASH_TEST_GROUP: "snapshot",
+    },
+  },
+});